After running KallistoQuant, I need to analyze my data on DeSeq2. The factors I have in my dataset are genotype (2 genotypes, WT and MUT) and treatment (3 treatments, R, L and V) and I would like to analyze them both separately (effect of treatment, effect on genotype) and together (treatment x genotype). I also have sex as a factor, but I am not interested in comparing M vs F for now. I have 35 samples in total, 3 per genotype, sex and treatment (except for 1 group in which I have 2). If I wanted to analyze only the males for now, how could I do it in Deseq2? IMPORTANT: I am not interested in comparing each group to all the others, but I have specific groups comparisons that I would like to do. Should I maybe use edgeR or limma instead of Deseq2? And how can I do it only on the males, if in the Kallisto dataset I have also the females? Could you please help me?